Adult brain retains the ability to produce new neurons throughout life. New neurons are generated from stem cells through a cascade of events which include symmetric and asymmetric divisions and continuous changes of cell morphology. The cascade culminates with the young neurons establishing connections with other cells and becoming integrated into the pre-existing neuronal circuitry. Persistent neurogenesis is observed only in a number of the adult brain regions. In one of them, the hippocampal dentate gyrus, new neurons may be important for learning, memory, and mood. Adult neurogenesis is a dynamic process that responds to a wide range of stimuli which can enhance or suppress its output and may affect any step of the differentiation cascade. For instance, an antidepressant drug fluoxetine (Prozac) enhances, whereas aging decreases, hippocampal neurogenesis. However, the steps of the differentiation cascade affected by pro- or anti-neurogenic factors and the mechanisms of their action are not known. The main goal of this collaborative project is to develop a computational model of adult neurogenesis. Towards this goal, we will develop a novel research method that integrates computational and experimental techniques for a quantitative investigation of the steps that define adult neurogenesis. A new approach developed in Enikolopov lab (experimental collaborator) uses a set of genetically encoded markers to monitor the progression of progenitor cells through the differentiation cascade. This approach allows to determine the abundances of different cell types as a function of time as the cells divide and differentiate. The abundances are evaluated only for cells that were dividing in the beginning of the experiment and correspond to the pair wise correlation function for different cell types. To convert the abundances as a function of time into the rates of division and differentiation of various cell types we will use the computational model developed by the group of Dr. Koulakov. This computational model will also be used to determine the effects of aging and antidepressants on the parameters of division and differentiation cascade. We will investigate the changes occurring in the genome-wide gene expression profiles as a function of stage of the differentiation cascade. We will monitor the dependence of gene expression on both aging and antidepressants and will elucidate the underlying gene regulation dynamics. Finally, we will study theoretically the putative computational properties of the adult neurogenesis.
The specific aims (SA) of this proposal include: SA 1: To develop a computational model for the stem cell division and differentiation cascade in the adult hippocampus.
This aim will allow inferring the division diagram and transition rates from the experimental data and will allow to study the changes induced by aging and antidepressants. SA 2: To dissect the transcription regulation network controlling adult hippocampal neurogenesis. We will investigate changes of gene expression associated with aging and antidepressant drugs and will uncover potential regulatory network mechanisms. SA 3: To study the unique computational properties of neural stem cells. Here we will calculate the rate of learning as a function of sparseness of representation and will argue that cell-based learning rules adopt to new stimuli faster than conventional synapse based Hebb rules. Intellectual merit: The proposed research will contribute to systems biology on two levels. First, we will elucidate the mechanisms of neural stem differentiation leading to the production of new neurons. Second, we will develop methods for determining division and differentiation rates from time-dependent data of cell abundances. This computational framework may become standard in the studies of stem cell differentiation in other fields of biology. Broader impacts: This project is based on the synergy between theoretical sciences, novel computational methods, and cutting-edge experiments in neurobiology. The award will provide a unique crossdisciplinary environment for training of young neuroscientists. We expect that two postdoctoral fellows, specializing in theoretical and in experimental approaches, will receive training through this award. To broader society: Our studies will help to elucidate the mechanisms of cognitive decline associated with aging and to determine the targets of antidepressant drug therapies. Because the lifetime incidence of depression in the US is more than 12% in men and 20% in women, our studies may substantially contribute to public health.

National Institute of Health (NIH)
National Institute of Mental Health (NIMH)
Research Project (R01)
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Special Emphasis Panel (ZRG1-IFCN-B (51))
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Panchision, David M
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Cold Spring Harbor Laboratory
Cold Spring Harbor
United States
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Shuvaev, Sergey A; Lazutkin, Alexander A; Kedrov, Alexander V et al. (2017) DALMATIAN: An Algorithm for Automatic Cell Detection and Counting in 3D. Front Neuroanat 11:117
Saboor, Farhan; Reckmann, Ansgar N; Tomczyk, Claudia U M et al. (2016) Nestin-expressing vascular wall cells drive development of pulmonary hypertension. Eur Respir J 47:876-88
Makaryus, Rany; Lee, Hedok; Feng, Tian et al. (2015) Brain maturation in neonatal rodents is impeded by sevoflurane anesthesia. Anesthesiology 123:557-68
Smagin, Dmitry A; Park, June-Hee; Michurina, Tatyana V et al. (2015) Altered Hippocampal Neurogenesis and Amygdalar Neuronal Activity in Adult Mice with Repeated Experience of Aggression. Front Neurosci 9:443
Wei, Yi; Koulakov, Alexei A (2014) Long-term memory stabilized by noise-induced rehearsal. J Neurosci 34:15804-15
Park, June-Hee; Lee, Hedok; Makaryus, Rany et al. (2014) Metabolic profiling of dividing cells in live rodent brain by proton magnetic resonance spectroscopy (1HMRS) and LCModel analysis. PLoS One 9:e94755
Birbrair, Alexander; Zhang, Tan; Wang, Zhong-Min et al. (2013) Role of pericytes in skeletal muscle regeneration and fat accumulation. Stem Cells Dev 22:2298-314
Birbrair, Alexander; Zhang, Tan; Wang, Zhong-Min et al. (2013) Skeletal muscle pericyte subtypes differ in their differentiation potential. Stem Cell Res 10:67-84
Park, June-Hee; Glass, Zachary; Sayed, Kasim et al. (2013) Calorie restriction alleviates the age-related decrease in neural progenitor cell division in the aging brain. Eur J Neurosci 37:1987-93
Flesken-Nikitin, Andrea; Hwang, Chang-Il; Cheng, Chieh-Yang et al. (2013) Ovarian surface epithelium at the junction area contains a cancer-prone stem cell niche. Nature 495:241-5

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